Available Skills

đź“– Table of Contents (click to expand)

This is the canonical index of all available AI agent skills in the bioconductor/ai-agent-skills repository. Use this to discover and understand what skills are available and when to use them.

Note: For instructions on how to use these skills, see the Skills Usage Guide. All skills are located at skills/{skill-name}/SKILL.md.

Meta Skills

Infrastructure and workflow skills for working with this repository itself.

adr-author

Purpose: Write a new Architecture Decision Record following the established Nygard format and conventions.

When to use:

  • Documenting a non-trivial, behavior-affecting decision
  • When you need to create an ADR

Invocation:

  • “Write an ADR for…”
  • “Record the decision to…”
  • “Document the design rationale for…”

Output: A new ADR file in the target repository’s docs/adr/ directory

create-skill

Purpose: Help create a new AI agent skill through collaborative Q&A

When to use:

  • Creating a new skill from scratch or from a manual workflow

Invocation:

  • “Help me create a new skill”
  • “Create a skill for [domain]”

Output: A complete skill with validated file and updated SKILLS.md, ready for testing and committing

Related skills: validate-skill, document-skill, check-bioconductor-skills

check-bioconductor-skills

Purpose: List and verify installed bioconductor skills

When to use:

  • Verifying skills are correctly installed or discovering available skills

Invocation:

  • “What skills are available?”
  • “List bioconductor skills”

Output: List of available skills and setup status

validate-skill

Purpose: Validate that a skill conforms to the ai-agent-skills repository standards

When to use:

  • Creating new skills, reviewing PRs, or ensuring standards compliance

Invocation:

  • “Validate this skill”
  • “Check if skills/[skill-name]/SKILL.md meets standards”

Output: Comprehensive validation report with pass/fail status, categorized issues, and specific fix suggestions

Related skills: create-skill, check-bioconductor-skills, document-skill

document-skill

Purpose: Automate documentation updates to SKILLS.md after creating or modifying a skill

When to use:

  • After creating a new skill or modifying an existing skill to update SKILLS.md

Invocation:

  • “Document the new skill I just created”
  • “Update SKILLS.md for the validate-r-docs skill”

Output: Updated SKILLS.md with the skill entry added to all relevant sections

Related skills: create-skill, validate-skill, check-bioconductor-skills

R/Bioconductor Package Skills

Skills for analyzing, documenting, and developing R/Bioconductor packages following bioconductor conventions.

analyze-r-package

Purpose: Analyze R/Bioconductor package structure and characteristics

When to use:

  • Understanding a package’s architecture, type, or identifying key functions

Invocation:

  • “Analyze this R package”
  • “What type of package is this?”

Output: Structured analysis of the package

create-package-instructions

Purpose: Generate comprehensive .github/instructions files for R/Bioconductor packages

When to use:

  • Creating AI agent instructions for a new R package or standardizing documentation

Invocation:

  • “Create .github/instructions for this package”
  • “Generate AI agent instructions”

Output: Modular instruction files in .github/instructions/

Related skills: analyze-r-package, update-package-instructions

update-package-instructions

Purpose: Update existing .github/instructions files based on recent package changes

When to use:

  • Refreshing package instructions after major architecture or pattern changes

Invocation:

  • “Update the package instructions”
  • “Refresh .github/instructions”

Output: Updated .github/instructions/ files

Related skills: analyze-r-package, create-package-instructions

improve-code-coverage

Purpose: Analyze R package code coverage using covr, classify testing gaps, and proactively write test cases.

When to use:

  • Evaluating testing rigor, identifying gaps, and proactively writing test cases

Invocation:

  • “Check my code coverage and help me write missing tests.”
  • “Improve code coverage, focusing on edge cases and correctness.”

Output: A chat summary breaking down coverage by test category, and code blocks containing testthat cases.

Related skills: analyze-r-package, security-audit-r-package

security-audit-r-package

Purpose: Perform comprehensive security audit of R/Bioconductor packages

When to use:

  • Auditing packages before CRAN/Bioconductor submission or reviewing for vulnerabilities

Invocation:

  • “Run security audit on this R package”
  • “Check this package for security vulnerabilities”

Output: Security audit report (markdown format) with findings categorized by severity.

Related skills: analyze-r-package, validate-skill, create-package-instructions

bioc-pkg-finder

Purpose: Find the R / Bioconductor packages best suited to a task or workflow

When to use:

  • When the user asks “what package should I use for X” or “is there a Bioconductor package that does Y”
  • Assembling an analysis workflow and needing to pick tools

Invocation:

  • “What package should I use for differential expression?”
  • “Is there a Bioconductor package that does single-cell clustering?”
  • “Which package is standard for variant annotation?”

Output: Recommended package(s) with biocViews term or CRAN Task View source, install path, and the key gotcha for the recommended tool

Related skills: analyze-r-package, create-package-instructions

update-r-news

Purpose: Draft or update an R package NEWS file from git commit history, examining diffs when commit messages are vague

Location: skills/update-r-news/SKILL.md

When to use:

  • Adding a NEWS entry before a Bioconductor release
  • Drafting a changelog from recent commits
  • Updating NEWS.md, NEWS, or NEWS.Rd after a development cycle
  • Saving time when commit messages alone are insufficient to write clear NEWS entries

What happens:

  • Detects the NEWS file format in use (NEWS.md, NEWS, or NEWS.Rd)
  • Derives the upcoming even-numbered release version from the current devel version
  • Finds the most recent Bioconductor devel-version bump commit (“bump x.y.z version to odd y…”) and retrieves all commits since then
  • Extracts PR titles from merge commits when available
  • Identifies vague commit messages (≤ 3 words or known filler phrases) and inspects their diffs to infer what changed
  • Categorises changes using headings already present in the NEWS file
  • Shows a full preview and asks for confirmation before writing to disk

Output: A drafted NEWS block shown for review; upon confirmation, the updated NEWS file on disk with the new version block prepended.

Related skills: analyze-r-package, update-package-instructions

Bioconductor How-Tos

Skills indexing focused, practical how-tos for common Bioconductor data analysis tasks.

bioc-howto

Purpose: A consolidated index of Bioconductor how-to skills covering genomics, sequencing, and omics data analysis tasks

When to use:

  • Looking for step-by-step instructions for common Bioconductor tasks (e.g., loading BAM files, manipulating GRanges, extracting sequences)
  • Needing examples of standard Bioconductor workflows

Invocation:

  • “How do I do [task] in Bioconductor?”
  • “Can you show me a Bioconductor how-to for [task]?”
  • “Check the bioc-howto index for [task]”

Output: Links to and instructions from the relevant how-to markdown file.

Skill Categories & Tags

By Category

Category Skills Purpose
meta adr-author, check-bioconductor-skills, create-skill, document-skill, validate-skill Repository and workflow infrastructure
r-packages analyze-r-package, bioc-pkg-finder, create-package-instructions, improve-code-coverage, security-audit-r-package, update-package-instructions, update-r-news R/Bioconductor package development
bioconductor-how-tos bioc-howto Bioconductor data analysis practical guides

By Tag

Tag Skills Use Case
infrastructure create-skill, check-bioconductor-skills, document-skill, validate-skill Repository and workflow tasks
testing improve-code-coverage Software testing and coverage
validation security-audit-r-package, validate-skill Quality control and standards compliance
quality-control security-audit-r-package, validate-skill Ensuring skill quality
documentation adr-author, create-package-instructions, document-skill, update-package-instructions, update-r-news Generating and maintaining docs
adr adr-author Architecture Decision Records
architecture adr-author Architectural decisions
decision adr-author Documenting decisions
automation document-skill, update-r-news Automating repetitive documentation tasks
analysis analyze-r-package, bioc-pkg-finder Understanding code and architecture
security security-audit-r-package Security audits and vulnerability detection
audit security-audit-r-package Comprehensive code auditing
bioconductor analyze-r-package, bioc-pkg-finder, create-package-instructions, improve-code-coverage, security-audit-r-package, update-package-instructions, update-r-news Bioconductor-specific workflows
code-coverage improve-code-coverage Code coverage analysis
covr improve-code-coverage Tools wrapping the covr package
data-access analyze-r-package (detects), create-package-instructions Working with remote data
git update-r-news Git-based workflows
changelog update-r-news Changelog and release note generation
news update-r-news R package NEWS file management
data-analysis bioc-howto Practical guides for analyzing omics data

Last Updated: 2026-07-17 Version: 2.0.2 Maintained by: bioconductor

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